Blast+ Sam outfmt parameter check

Question

[larvalanobium]

Good day

I am working with the blast+ command line tools and struggling to get my result of a blast search to come back in a sam file with the actual sequence data (not just the sequence identifiers).

This is my command

blastn -db nt -query QUERY.fas -out theten -entrez_query "$EQ" -outfmt 17 SQ -max_target_seqs 10 -remote

With the SQ argument after the the option value 17 for -outfmt. This should return a sam file with sequence data included, but I'm getting back sam files with only the sequence identifiers. I've tried putting the SQ argument before the 17 and still get the same result.

Can anyone help with this?

Thanks and kind regards Crystal

[glihm]

Why are you using this "SQ"? Did you find this in some documentation?

Because "SQ" refers to headers (sequences)... and for me, in the version 2.6.0+, your command line triggers this error:

Too many positional arguments (1), the offending value: SQ

In local use, the command:

blastn -db db.fa -query query.fa -out theten -outfmt 17

works well and outputs a well formatted SAM file with headers + data.

[larvalanobium]

Thanks for replying!

The documentation where I found the SQ argument for the -outfmt parameter is from the blastn -help.

The problem is that I don't get the actual sequences in the sam file (just the identifiers).

Maybe it is a problem using the remote server vs a local database. Does your output look the same if you use remote option?

Thanks and kind regards Crystal

[Aqua_4_2]

In order to avoid this error, the command needs to be formatted as:

blastn -db db.fa -query query.fa -out theten -outfmt "17 SQ"

This gives the desired sequence data in the sam file, along with the identifiers. I've tried this on a remote server and it worked well.